[phenixbb] labelit access in Phenix?

R.D. Oeffner rdo20 at cam.ac.uk
Sun Jun 28 14:54:35 PDT 2015

This should have been forward to the mailing list.


-------- Original Message --------
Subject: Re: [phenixbb] labelit access in Phenix?
Date: 2015-06-26 21:46
 From: "R.D. Oeffner" <rdo20 at cam.ac.uk>
To: "Keller, Jacob" <kellerj at janelia.hhmi.org>
Copy: Aaron Brewster <asbrewster at lbl.gov>, Nigel W Moriarty 
<NWMoriarty at lbl.gov>

Hi Jacob,

Labelit is not present on Windows in the last official release of Phenix 
from May last year, version 1.9-1692. But it is present in recent 
pre-releases of Phenix as command line tools.

When you install Phenix on Windows a startup group is created that 
includes a command line prompt which recognises Phenix commands. From 
there you can execute all labelit command line tools.

I think Nigel is about to put the recent Windows pre-release online on 
the Phenix website.

Feel free to get in touch with further questions.



On 2015-06-26 18:44, Aaron Brewster wrote:
> Hi Jacob, replying off of the list for now.  There is no labelit gui
> support in the phenix gui.  There may be a batch script you have to
> run to get the phenix command line binaries in the path for the cmd
> program in win7, but I don't know it.  If you can run phenix.refine on
> the command line but not labelit, that would be instructive.
> cc'ing Rob who has been working on the phenix windows build.
> -Aaron
> On Thu, Jun 25, 2015 at 7:58 PM, Keller, Jacob
> <kellerj at janelia.hhmi.org> wrote:
>> Dear Phenix list,
>> Does anyone know how to access labelit through Phenix to determine
>> whether the highest possible symmetry has been found? I exclusively
>> use the GUI, and it's on win7.
>> In the labelit documentation/homepage it mentions the command:
>> labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file]
>> But I did not find any executables called labelit, nor can I figure
>> out how to run Phenix from command line in Win7, short of installing
>> Cygwin or something.
>> JPK
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